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I am having problems reproducing this issue. I created a fedRoot db, then created a federation member. I migrated from SQL Server (adding FEDERATED ON) to the script on the ids that I wanted to federate on. That process went well and then I did a split for
fun and everything went well. Then I used SQLAzureMW to generate script from my federation to a new federation and everything there worked great as well.

So I am not sure what is going on. Would it be possible for you to send me the generated script so I can look at it?

Ahhh Ha! I figured it out. I bet you are running with v4.0.16.1 (the code built on SQL Server 2012 libraries). While I was running on v3.9.13.1 (code build on SQL Server 2008 R2 SP1). The difference is that SQL Server 2012 is federation aware and when
SMO generates the script, it puts the FEDERATED ON statement on the CREATE TABLE. Whereas SQL Server 2008 R2 SP1 is not federation aware and I had to check federation meta data and figure out which table / column was used for federations and add my own FEDERATED
ON clause. So, I now know what I need to fix. If you want to run, use v3.9.13.1 for now and I will post a fix soon.